# Generated by roxygen2: do not edit by hand

export(binomial_test)
export(cluster_signatures)
export(cos_sim)
export(cos_sim_matrix)
export(enrichment_depletion_test)
export(extract_signatures)
export(fit_to_signatures)
export(genomic_distribution)
export(mut_context)
export(mut_matrix)
export(mut_matrix_stranded)
export(mut_strand)
export(mut_type)
export(mut_type_occurrences)
export(mutation_context)
export(mutation_types)
export(mutations_from_vcf)
export(plot_192_profile)
export(plot_96_profile)
export(plot_compare_profiles)
export(plot_contribution)
export(plot_contribution_heatmap)
export(plot_cosine_heatmap)
export(plot_enrichment_depletion)
export(plot_rainfall)
export(plot_signature_strand_bias)
export(plot_spectrum)
export(plot_strand)
export(plot_strand_bias)
export(read_vcfs_as_granges)
export(strand_bias_test)
export(strand_from_vcf)
export(strand_occurrences)
export(type_context)
import(GenomicRanges)
import(NMF)
import(ggplot2)
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,match)
importFrom(BiocGenerics,rbind)
importFrom(Biostrings,getSeq)
importFrom(GenomeInfoDb,"organism")
importFrom(GenomeInfoDb,"seqlevelsStyle<-")
importFrom(GenomeInfoDb,extractSeqlevelsByGroup)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicRanges,reduce)
importFrom(IRanges,reverse)
importFrom(S4Vectors,isEmpty)
importFrom(SummarizedExperiment,rowRanges)
importFrom(VariantAnnotation,readVcf)
importFrom(cowplot,plot_grid)
importFrom(ggdendro,dendro_data)
importFrom(ggdendro,segment)
importFrom(ggdendro,theme_dendro)
importFrom(parallel,detectCores)
importFrom(parallel,mclapply)
importFrom(plyr,.)
importFrom(plyr,adply)
importFrom(plyr,ddply)
importFrom(plyr,llply)
importFrom(plyr,summarise)
importFrom(pracma,lsqnonneg)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(stats,"poisson.test")
importFrom(stats,aggregate)
importFrom(stats,pbinom)
importFrom(stats,sd)
